ATP6V0A1

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0016471 vacuolar proton-transporting V-type ATPase complex	IBA GO_REF:0000033	ACCEPT	Summary: Correct core complex annotation. ATP6V0A1 is a subunit of the V0 membrane sector of the vacuolar proton-transporting V-type ATPase complex. Reason: The UniProt record and human V-ATPase structure place ATP6V0A1 in the V0 proton-translocation sector of the assembled V-ATPase complex. Supporting Evidence: file:human/ATP6V0A1/ATP6V0A1-uniprot.txt proton transport subunit a, a ring of proteolipid subunits PMID:33065002 Here, we report cryo-EM structures of a human V-ATPase
GO:0046961 proton-transporting ATPase activity, rotational mechanism	IBA GO_REF:0000033	ACCEPT	Summary: Correct as a contributes_to annotation. ATP6V0A1 is not an isolated catalytic ATPase, but as the V0 a-subunit it contributes to the rotary proton-pumping activity of the complete V-ATPase. Reason: Human V-ATPase is an ATP-driven proton pump; the a-subunit is part of the membrane proton-translocation domain that couples to V1 ATP hydrolysis. Supporting Evidence: PMID:33065002 ATP hydrolysis-driven proton pumps that acidify intracellular vesicles PMID:34909687 responsible for proton translocation
GO:0005886 plasma membrane	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: Supported but not core for ATP6V0A1. V-ATPases can be present at the plasma membrane in specialized contexts, but the main ATP6V0A1 function is organellar acidification. Reason: Keep as a specialized-cell localization rather than a core location for the a1 isoform. Supporting Evidence: file:human/ATP6V0A1/ATP6V0A1-uniprot.txt certain cell types, can be exported to the plasma membrane
GO:0007035 vacuolar acidification	IBA GO_REF:0000033	ACCEPT	Summary: Correct core biological process. ATP6V0A1 contributes to V-ATPase-mediated acidification of intracellular organelles. Reason: Although lysosomal and endosomal terms are more precise in mammalian cells, vacuolar acidification captures the conserved V-ATPase role in organelle lumen acidification. Supporting Evidence: file:human/ATP6V0A1/ATP6V0A1-uniprot.txt acidification of various organelles, such as lysosomes, endosomes PMID:33833240 These data suggested that all ATP6V0A1 missense variants impaired lysosomal acidification in cell lines.
GO:0051117 ATPase binding	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: Supported V0-V1 interface annotation, but non-core. ATP6V0A1 binds V1-sector ATPase subunits as part of V-ATPase assembly/regulation; this interaction is secondary to the proton-pump function. Reason: The ATPase-binding term captures a real subunit-interface property but should not displace the complex-level proton transport function as the core molecular role. Supporting Evidence: PMID:17360703 These interactions represent a novel link between the V(1) and V(0) domains in man
GO:0000220 vacuolar proton-transporting V-type ATPase, V0 domain	IEA GO_REF:0000002	ACCEPT	Summary: Correct V0-domain component annotation from InterPro. ATP6V0A1 is the a-subunit of the V0 membrane sector. Reason: The V0-domain annotation is central to ATP6V0A1 identity and is supported by UniProt and human V-ATPase structural work. Supporting Evidence: file:human/ATP6V0A1/ATP6V0A1-uniprot.txt proton transport subunit a, a ring of proteolipid subunits
GO:0030665 clathrin-coated vesicle membrane	IEA GO_REF:0000044	KEEP AS NON CORE	Summary: Plausible non-core localization. UniProt maps ATP6V0A1 to clathrin-coated vesicle membrane by similarity, consistent with V-ATPase function in vesicular compartments. Reason: This is a specific vesicle-membrane localization, but the core localization/function is broader endolysosomal and synaptic vesicle acidification. Supporting Evidence: file:human/ATP6V0A1/ATP6V0A1-uniprot.txt secretory vesicle, synaptic vesicle
GO:0030672 synaptic vesicle membrane	IEA GO_REF:0000044	ACCEPT	Summary: Correct neuronal vesicle localization. ATP6V0A1 is annotated to synaptic vesicle membrane, and mutant mouse evidence supports a role in synaptic vesicle proton-dependent neurotransmitter loading. Reason: The a1 isoform is brain enriched and supports proton-gradient-dependent synaptic vesicle function. Supporting Evidence: file:human/ATP6V0A1/ATP6V0A1-uniprot.txt secretory vesicle, synaptic vesicle PMID:33833240 the neurotransmitter content of synaptic vesicles was indeed lowered in Atp6v0a1A512P/A512P mice, presumably due to the reduced proton pump activity.
GO:0033179 proton-transporting V-type ATPase, V0 domain	IEA GO_REF:0000002	ACCEPT	Summary: Correct V0-domain component annotation. This is the generic V0-domain term and is already consistent with the PN projection. Reason: ATP6V0A1 is the a-subunit of the V0 proton-translocation sector of V-ATPase. Supporting Evidence: file:human/ATP6V0A1/ATP6V0A1-uniprot.txt proton transport subunit a, a ring of proteolipid subunits
GO:0042470 melanosome	IEA GO_REF:0000044	KEEP AS NON CORE	Summary: Supported but non-core localization. ATP6V0A1 was identified in melanosome fractions, but melanosomes are a specialized lysosome-related organelle context rather than the core role of the gene. Reason: Retain melanosome localization as a specialized organelle location supported by proteomics and UniProt, not as the main ATP6V0A1 function. Supporting Evidence: file:human/ATP6V0A1/ATP6V0A1-uniprot.txt melanosome fractions from stage I to stage IV PMID:12643545 identify protein components of early melanosomes
GO:0046961 proton-transporting ATPase activity, rotational mechanism	IEA GO_REF:0000002	MODIFY	Summary: Correct V-ATPase activity term. ATP6V0A1 contributes to the rotary proton-pumping activity of the complete V-ATPase; the term is appropriate when interpreted in the complex-subunit context already captured by the IBA contributes_to row. Reason: The GO term itself is correct for the V-ATPase complex activity, but the IEA qualifier should be changed from enables to contributes_to because ATP6V0A1 is a V0-sector subunit rather than an isolated catalytic ATPase. Proposed replacements: proton-transporting ATPase activity, rotational mechanism Supporting Evidence: PMID:33065002 ATP hydrolysis-driven proton pumps that acidify intracellular vesicles
GO:1902600 proton transmembrane transport	IEA GO_REF:0000002	ACCEPT	Summary: Correct core process. The V0 a-subunit participates directly in proton transmembrane transport across organelle membranes. Reason: ATP6V0A1 is part of the membrane proton-translocation domain, and pathogenic variants perturb proton translocation/acidification. Supporting Evidence: file:human/ATP6V0A1/ATP6V0A1-uniprot.txt proton transport subunit a, a ring of proteolipid subunits PMID:34909687 responsible for proton translocation
GO:0005515 protein binding	IPI PMID:7896830 Vacuolar H(+)-ATPase mutants transform cells and define a bi...	REMOVE	Summary: Remove. The cited publication defines binding of papillomavirus E5 to the 16 kDa V-ATPase proteolipid subunit, not ATP6V0A1/a1. Reason: This appears to be a mismatched or over-propagated protein-binding annotation. ATP6V0A1 has other valid interaction evidence, but PMID:7896830 does not support ATP6V0A1 protein binding. Supporting Evidence: PMID:7896830 The 16K subunit of the vacuolar H(+)-ATPase binds specifically
GO:0005737 cytoplasm	IEA GO_REF:0000107	MARK AS OVER ANNOTATED	Summary: Too broad. ATP6V0A1 has cytoplasmic domains but is a multi-pass membrane V-ATPase subunit; cytoplasm alone loses the informative membrane/complex localization. Reason: Prefer membrane-sector and organelle membrane annotations over a broad cytoplasm location. Supporting Evidence: file:human/ATP6V0A1/ATP6V0A1-uniprot.txt Required for assembly and activity of the vacuolar ATPase
GO:0048471 perinuclear region of cytoplasm	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Plausible but non-core transferred localization. Perinuclear cytoplasm is compatible with endolysosomal/Golgi-region organelles but is less informative than the specific membrane compartments. Reason: Keep as broad cellular context from orthology transfer, while relying on lysosomal/endosomal/synaptic vesicle membrane terms for core localization. Supporting Evidence: file:human/ATP6V0A1/ATP6V0A1-uniprot.txt acidification of various organelles, such as lysosomes, endosomes
GO:0097401 synaptic vesicle lumen acidification	IEA GO_REF:0000107	ACCEPT	Summary: Correct neuronal process. ATP6V0A1 supports synaptic vesicle proton gradients needed for neurotransmitter loading. Reason: Mouse variant data show lowered synaptic vesicle neurotransmitter content, consistent with reduced V-ATPase proton-pump activity. Supporting Evidence: PMID:33833240 the neurotransmitter content of synaptic vesicles was indeed lowered in Atp6v0a1A512P/A512P mice, presumably due to the reduced proton pump activity. file:human/ATP6V0A1/ATP6V0A1-uniprot.txt secretory vesicle, synaptic vesicle
GO:0007042 lysosomal lumen acidification	NAS PMID:33065002 Structures of a Complete Human V-ATPase Reveal Mechanisms of...	ACCEPT	Summary: Correct core lysosomal process. Human ATP6V0A1 variants impair lysosomal acidification, and the V-ATPase complex maintains lysosomal pH. Reason: This is one of the strongest ATP6V0A1 process annotations and is directly aligned with the PN lysosomal acidification row. Supporting Evidence: PMID:33065002 pH homeostasis of endosomes and lysosomes PMID:33833240 These data suggested that all ATP6V0A1 missense variants impaired lysosomal acidification in cell lines. PMID:34909687 direct impairment of endolysosome acidification and failure of lysosomal functions.
GO:0016020 membrane	IDA PMID:33065002 Structures of a Complete Human V-ATPase Reveal Mechanisms of...	MARK AS OVER ANNOTATED	Summary: Correct but too broad. ATP6V0A1 is a membrane protein, but generic membrane does not capture its V0-sector/endolysosomal and vesicular membrane identity. Reason: Use specific V-ATPase complex and organelle membrane annotations where possible. Supporting Evidence: file:human/ATP6V0A1/ATP6V0A1-uniprot.txt Required for assembly and activity of the vacuolar ATPase
GO:0033176 proton-transporting V-type ATPase complex	NAS PMID:33065002 Structures of a Complete Human V-ATPase Reveal Mechanisms of...	ACCEPT	Summary: Correct complex annotation. ATP6V0A1 is part of the proton-transporting V-type ATPase complex described structurally in human cells. Reason: The complete human V-ATPase structure and UniProt subunit summary support complex membership. Supporting Evidence: PMID:33065002 Here, we report cryo-EM structures of a human V-ATPase file:human/ATP6V0A1/ATP6V0A1-uniprot.txt proton transport subunit a, a ring of proteolipid subunits
GO:0048388 endosomal lumen acidification	NAS PMID:32001091 Structure and Roles of V-type ATPases.	ACCEPT	Summary: Correct process annotation. V-ATPase acidifies endosomes, and ATP6V0A1 contributes to the proton-translocation sector. Reason: Endosomal acidification is a core organelle-acidification output of V-ATPase. Supporting Evidence: file:human/ATP6V0A1/ATP6V0A1-uniprot.txt acidification of various organelles, such as lysosomes, endosomes PMID:33065002 pH homeostasis of endosomes and lysosomes Reactome:R-HSA-74723 The effect of the proton pump is to allow entry of [H+] ions into the lumen of the endosome.
GO:1902600 proton transmembrane transport	NAS PMID:33065002 Structures of a Complete Human V-ATPase Reveal Mechanisms of...	ACCEPT	Summary: Correct core process. ATP6V0A1 contributes to ATP-driven proton transport across cellular membranes. Reason: This process is supported by V-ATPase structure/function literature and ATP6V0A1 disease variants that impair acidification. Supporting Evidence: PMID:33065002 ATP hydrolysis-driven proton pumps that acidify intracellular vesicles PMID:34909687 responsible for proton translocation
GO:0042470 melanosome	EXP PMID:12643545 Proteomic analysis of early melanosomes: identification of n...	KEEP AS NON CORE	Summary: Supported but non-core localization from melanosome proteomics. Reason: Melanosome localization is experimentally supported, but it is a specialized lysosome-related organelle location rather than the main ATP6V0A1 role. Supporting Evidence: file:human/ATP6V0A1/ATP6V0A1-uniprot.txt melanosome fractions from stage I to stage IV PMID:12643545 identify protein components of early melanosomes
GO:0042470 melanosome	EXP PMID:17081065 Proteomic and bioinformatic characterization of the biogenes...	KEEP AS NON CORE	Summary: Supported but non-core localization from melanosome proteomics across developmental stages. Reason: Retain as specialized lysosome-related organelle localization; do not treat as the core function. Supporting Evidence: file:human/ATP6V0A1/ATP6V0A1-uniprot.txt melanosome fractions from stage I to stage IV PMID:17081065 melanosome proteomes at various developmental stages
GO:0000220 vacuolar proton-transporting V-type ATPase, V0 domain	ISS GO_REF:0000024	ACCEPT	Summary: Correct orthology-supported V0-domain annotation. Reason: The V0-domain role is conserved across V-ATPase a-subunit family members and supported by the human UniProt record. Supporting Evidence: file:human/ATP6V0A1/ATP6V0A1-uniprot.txt proton transport subunit a, a ring of proteolipid subunits file:interpro/panther/PTHR11629/PTHR11629-metadata.yaml VACUOLAR PROTON ATPASES
GO:0005765 lysosomal membrane	TAS PMID:22982048 Lipofuscin is formed independently of macroautophagy and lys...	ACCEPT	Summary: Correct lysosomal membrane localization. Although the original TAS citation is indirect, ATP6V0A1 localization and functional evidence strongly support lysosomal V-ATPase membership. Reason: ATP6V0A1 localizes with lysosomal V-ATPase in cell assays and disease variants impair lysosomal acidification. Supporting Evidence: PMID:33833240 These data suggested that all ATP6V0A1 missense variants impaired lysosomal acidification in cell lines. file:human/ATP6V0A1/ATP6V0A1-uniprot.txt acidification of various organelles, such as lysosomes, endosomes
GO:0005886 plasma membrane	TAS Reactome:R-HSA-6798743	KEEP AS NON CORE	Summary: Supported specialized-cell localization. Reactome places V-ATPase-containing secretory vesicle membranes at the plasma membrane during degranulation. Reason: This is a contextual trafficking/localization annotation and not the primary ATP6V0A1 function. Supporting Evidence: Reactome:R-HSA-6798743 Secretory vesicles provide a reservoir of membrane-associated receptors file:human/ATP6V0A1/ATP6V0A1-uniprot.txt certain cell types, can be exported to the plasma membrane
GO:0005886 plasma membrane	TAS Reactome:R-HSA-6800426	KEEP AS NON CORE	Summary: Supported specialized neutrophil granule/plasma membrane context, but non-core. Reason: Retain as a Reactome-derived specialized localization while keeping organelle acidification as the core role. Supporting Evidence: Reactome:R-HSA-6800426 Ficoli-1 rich granules are a relatively new fourth neutrophil granule population file:human/ATP6V0A1/ATP6V0A1-uniprot.txt certain cell types, can be exported to the plasma membrane
GO:0030667 secretory granule membrane	TAS Reactome:R-HSA-6798743	KEEP AS NON CORE	Summary: Supported secretory granule membrane context for V-ATPase-containing vesicles, but non-core. Reason: Secretory granules are one organelle class acidified by V-ATPase; this is narrower cellular context rather than a separate core function. Supporting Evidence: Reactome:R-HSA-6798743 Secretory vesicles provide a reservoir of membrane-associated receptors file:human/ATP6V0A1/ATP6V0A1-uniprot.txt acidification of various organelles, such as lysosomes, endosomes
GO:0101003 ficolin-1-rich granule membrane	TAS Reactome:R-HSA-6800426	KEEP AS NON CORE	Summary: Supported ficolin-1-rich granule membrane context in neutrophil degranulation, but non-core. Reason: This specific granule class is a specialized immune-cell localization; ATP6V0A1 core function remains V-ATPase proton transport. Supporting Evidence: Reactome:R-HSA-6800426 Ficoli-1 rich granules are a relatively new fourth neutrophil granule population file:human/ATP6V0A1/ATP6V0A1-uniprot.txt acidification of various organelles, such as lysosomes, endosomes
GO:0007035 vacuolar acidification	TAS PMID:22982048 Lipofuscin is formed independently of macroautophagy and lys...	ACCEPT	Summary: Correct organelle acidification process. The original lipofuscin paper is indirect for ATP6V0A1, but independent ATP6V0A1 and V-ATPase evidence strongly supports vacuolar/endolysosomal acidification. Reason: Retain the process because it is supported by direct ATP6V0A1 mutant acidification assays and general V-ATPase structure/function evidence. Supporting Evidence: PMID:33833240 These data suggested that all ATP6V0A1 missense variants impaired lysosomal acidification in cell lines. PMID:33065002 ATP hydrolysis-driven proton pumps that acidify intracellular vesicles
GO:0016241 regulation of macroautophagy	IMP PMID:22982048 Lipofuscin is formed independently of macroautophagy and lys...	KEEP AS NON CORE	Summary: Keep as non-core. V-ATPase dysfunction causes autophagy defects, but this reflects lysosomal/endolysosomal acidification and autophagic flux rather than ATP6V0A1 acting as a dedicated macroautophagy regulator. Reason: Aoto and Bott show autophagy defects when ATP6V0A1/V-ATPase function is impaired; the direct core function is proton pumping and organelle acidification. Supporting Evidence: PMID:33833240 Lysosomal dysfunction resulting in cell death, impaired autophagy, and reduced mTORC1 signaling and synaptic connectivity PMID:22982048 macroautophagy is responsible for the uptake of lipofuscin into the lysosomes. PMID:28024296 localized to the late endosome/lysosome and interacts with the lysosomal v-ATPase to negatively regulate mTORC1 activation
GO:0070062 extracellular exosome	HDA PMID:23533145 In-depth proteomic analyses of exosomes isolated from expres...	MARK AS OVER ANNOTATED	Summary: High-throughput exosome localization, not a core ATP6V0A1 compartment. Reason: Exosome proteomics can reflect vesicular trafficking or membrane protein carryover; it does not define the main site of ATP6V0A1 function. Supporting Evidence: PMID:23533145 exosome preparations were characterized by a shotgun proteomics procedure.
GO:0070062 extracellular exosome	HDA PMID:19056867 Large-scale proteomics and phosphoproteomics of urinary exos...	MARK AS OVER ANNOTATED	Summary: High-throughput urinary exosome localization, not a core ATP6V0A1 compartment. Reason: Retain the evidence as a high-throughput detection but do not treat extracellular exosome as a primary functional localization. Supporting Evidence: PMID:19056867 Here, we used LC-MS/MS to profile the proteome of human urinary exosomes.
GO:0030670 phagocytic vesicle membrane	TAS Reactome:R-HSA-1222516	KEEP AS NON CORE	Summary: Supported specialized phagocytic vesicle membrane context. V-ATPase acidifies phagosomes, but this is a cell-context-specific location. Reason: Reactome supports V-ATPase-driven phagosomal acidification; the annotation should remain secondary to the general endolysosomal/synaptic vesicle acidification function. Supporting Evidence: Reactome:R-HSA-1222516 ATP hydrolysis drives a 120 degree rotation of the rotor which leads to movement of three protons into the phagosome PMID:33065002 ATP hydrolysis-driven proton pumps that acidify intracellular vesicles
GO:0010008 endosome membrane	TAS Reactome:R-HSA-5252133	ACCEPT	Summary: Correct endosome membrane localization in a V-ATPase assembly/accessory-subunit pathway context. Reason: ATP6V0A1 contributes to V-ATPase complexes on endosomal membranes where proton pumping acidifies the endosomal lumen. Supporting Evidence: PMID:33065002 pH homeostasis of endosomes and lysosomes
GO:0010008 endosome membrane	TAS Reactome:R-HSA-74723	ACCEPT	Summary: Correct endosome membrane localization for endosome acidification. Reason: Endosome membrane is a core V-ATPase location and directly matches endosomal acidification evidence. Supporting Evidence: Reactome:R-HSA-74723 The effect of the proton pump is to allow entry of [H+] ions into the lumen of the endosome. PMID:33065002 pH homeostasis of endosomes and lysosomes
GO:0010008 endosome membrane	TAS Reactome:R-HSA-917841	ACCEPT	Summary: Correct endosome membrane localization in transferrin receptor endosome acidification. Reason: This is a specific Reactome endosomal acidification context for the same core V-ATPase function. Supporting Evidence: Reactome:R-HSA-917841 Acidification of Tf:TfR1 containing endosome PMID:33065002 pH homeostasis of endosomes and lysosomes
GO:0005886 plasma membrane	IDA PMID:17360703 V1 and V0 domains of the human H+-ATPase are linked by an in...	KEEP AS NON CORE	Summary: Supported but non-core plasma membrane localization. The cited interaction work supports V0-V1 linkage, while UniProt treats plasma membrane export as cell-type-specific. Reason: Use as specialized localization context only; organelle membrane acidification remains the primary role. Supporting Evidence: PMID:17360703 These interactions represent a novel link between the V(1) and V(0) domains in man file:human/ATP6V0A1/ATP6V0A1-uniprot.txt certain cell types, can be exported to the plasma membrane
GO:0051117 ATPase binding	IPI PMID:17360703 V1 and V0 domains of the human H+-ATPase are linked by an in...	KEEP AS NON CORE	Summary: Supported V0-V1 interaction with ATP6V1G1/G1, but non-core molecular function. Reason: The G-subunit/a-subunit interaction links V1 and V0 domains and is relevant to assembly/regulation, but proton transport is the core function. Supporting Evidence: PMID:17360703 These interactions represent a novel link between the V(1) and V(0) domains in man
GO:0051117 ATPase binding	IPI PMID:17360703 V1 and V0 domains of the human H+-ATPase are linked by an in...	KEEP AS NON CORE	Summary: Supported V0-V1 interaction with ATP6V1G3/G3, but non-core molecular function. Reason: The G-subunit/a-subunit interaction links V1 and V0 domains and is relevant to assembly/regulation, but proton transport is the core function. Supporting Evidence: PMID:17360703 similar G1/a1, G3/a1, and G1/a4 interactions were also demonstrated
GO:0005515 protein binding	IPI PMID:12649290 The a-subunit of the V-type H+-ATPase interacts with phospho...	MARK AS OVER ANNOTATED	Summary: The PFK-1 interaction with the a1 subunit is supported, but generic protein binding is an uninformative over-annotation for ATP6V0A1. Reason: Keep the interaction as context for possible metabolic regulation, but do not treat generic protein binding as a core molecular function. Supporting Evidence: PMID:12649290 An in vitro bead-bound PFK-1 pull-down assay showed that this interaction was also true for the ubiquitously expressed a1 subunit.
GO:0046610 lysosomal proton-transporting V-type ATPase, V0 domain	IC file:projects/PROTEOSTASIS/reports/pn_projection/pn_projected_candidate_additions.tsv	NEW	Summary: NEW annotation from conservative PN projection review. ATP6V0A1 already has generic V0-domain and lysosomal membrane/acidification annotations; GO:0046610 adds the lysosomal V0-domain specificity supported by the PN row and independent ATP6V0A1/V-ATPase evidence. Reason: The PN candidate is not accepted merely by propagation. It is retained because ATP6V0A1 is a V0-sector a-subunit, V-ATPase operates on lysosomal/endolysosomal membranes, and ATP6V0A1 variants directly impair lysosomal/endolysosomal acidification. Supporting Evidence: file:projects/PROTEOSTASIS/reports/pn_projection/pn_projected_candidate_additions.tsv ATP6V0A1 GO:0046610 lysosomal proton-transporting V-type ATPase, V0 domain file:human/ATP6V0A1/ATP6V0A1-uniprot.txt proton transport subunit a, a ring of proteolipid subunits PMID:33833240 These data suggested that all ATP6V0A1 missense variants impaired lysosomal acidification in cell lines. PMID:34909687 direct impairment of endolysosome acidification and failure of lysosomal functions.

Gene Description

Existing Annotations Review

Core Functions

ATP6V0A1 is the a1 subunit of the V0 membrane sector of V-ATPase and contributes to rotary ATP-driven proton transport by the assembled complex.

As part of V-ATPase complexes on endolysosomal and synaptic vesicle membranes, ATP6V0A1 supports acidification of lysosomes, endosomes, and synaptic vesicles, with downstream effects on protein degradation, autophagic flux, mTORC1/Notch signaling contexts, and neurotransmitter loading.

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